From bfa67dbdf835a59598d6a1418af9bea514a36bc8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 7 Mar 2013 21:22:06 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9614 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 42 +++++++++++++++++++-------------------- doc/Section_commands.txt | 6 ++++-- doc/Section_errors.html | 8 ++++---- doc/Section_errors.txt | 8 ++++---- doc/Section_howto.html | 4 ++-- doc/Section_howto.txt | 4 ++-- doc/Section_python.html | 2 +- doc/Section_python.txt | 2 +- doc/kspace_style.html | 2 +- doc/kspace_style.txt | 2 +- doc/pair_coeff.html | 25 +++++++++++++++++------ doc/pair_coeff.txt | 25 +++++++++++++++++------ doc/pair_lj.html | 39 +++++++++++++++++++++++++----------- doc/pair_lj.txt | 37 +++++++++++++++++++++++----------- doc/pair_style.html | 21 ++++++++++++++++---- doc/pair_style.txt | 21 ++++++++++++++++---- 16 files changed, 165 insertions(+), 83 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 10842f7b54..107bfe1a60 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -456,14 +456,14 @@ potentials. Click on the style itself for a full description: line/ljlj/charmm/coul/charmmlj/charmm/coul/charmm/implicitlj/charmm/coul/long lj/charmm/coul/msmlj/class2lj/class2/coul/cutlj/class2/coul/long lj/cutlj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/dsf -lj/cut/coul/longlj/cut/coul/msmlj/long/coul/longlj/cut/tip4p/long -lj/long/tip4p/longlj/expandlj/gromacslj/gromacs/coul/gromacs -lj/smoothlj/smooth/linearlj96/cutlubricate -lubricate/polylubricateUlubricateU/polymeam -mie/cutmorseperi/lpsperi/pmb -reaxreboresquaredsoft -swtabletersofftersoff/zbl -tri/ljyukawayukawa/colloid +lj/cut/coul/longlj/cut/coul/msmlj/cut/tip4p/cutlj/cut/tip4p/long +lj/expandlj/gromacslj/gromacs/coul/gromacslj/long/coul/long +lj/long/tip4p/longlj/smoothlj/smooth/linearlj96/cut +lubricatelubricate/polylubricateUlubricateU/poly +meammie/cutmorseperi/lps +peri/pmbreaxreboresquared +softswtabletersoff +tersoff/zbltri/ljyukawayukawa/colloid

These are pair styles contributed by users, which can be used if @@ -509,19 +509,19 @@ package. lj/cut/coul/debye/gpulj/cut/coul/debye/omplj/cut/coul/dsf/gpulj/cut/coul/long/cuda lj/cut/coul/long/gpulj/cut/coul/long/omplj/cut/coul/long/optlj/cut/coul/msm/opt lj/cut/cudalj/cut/experimental/cudalj/cut/gpulj/cut/omp -lj/cut/optlj/cut/tip4p/long/omplj/cut/tip4p/long/optlj/expand/cuda -lj/expand/gpulj/expand/omplj/gromacs/coul/gromacs/cudalj/gromacs/coul/gromacs/omp -lj/gromacs/cudalj/gromacs/omplj/long/coul/long/optlj/sdk/gpu -lj/sdk/omplj/sdk/coul/long/gpulj/sdk/coul/long/omplj/sdk/coul/msm/omp -lj/sf/omplj/smooth/cudalj/smooth/omplj/smooth/linear/omp -lj96/cut/cudalj96/cut/gpulj96/cut/omplubricate/omp -lubricate/poly/ompmeam/spline/ompmorse/cudamorse/gpu -morse/ompmorse/optperi/lps/ompperi/pmb/omp -rebo/ompresquared/gpuresquared/ompsoft/omp -sw/cudasw/omptable/gputable/omp -tersoff/cudatersoff/omptersoff/table/omptersoff/zbl/omp -tri/lj/ompyukawa/gpuyukawa/ompyukawa/colloid/gpu -yukawa/colloid/omp +lj/cut/optlj/cut/tip4p/cut/omplj/cut/tip4p/long/omplj/cut/tip4p/long/opt +lj/expand/cudalj/expand/gpulj/expand/omplj/gromacs/coul/gromacs/cuda +lj/gromacs/coul/gromacs/omplj/gromacs/cudalj/gromacs/omplj/long/coul/long/opt +lj/sdk/gpulj/sdk/omplj/sdk/coul/long/gpulj/sdk/coul/long/omp +lj/sdk/coul/msm/omplj/sf/omplj/smooth/cudalj/smooth/omp +lj/smooth/linear/omplj96/cut/cudalj96/cut/gpulj96/cut/omp +lubricate/omplubricate/poly/ompmeam/spline/ompmorse/cuda +morse/gpumorse/ompmorse/optperi/lps/omp +peri/pmb/omprebo/ompresquared/gpuresquared/omp +soft/ompsw/cudasw/omptable/gpu +table/omptersoff/cudatersoff/omptersoff/table/omp +tersoff/zbl/omptri/lj/ompyukawa/gpuyukawa/omp +yukawa/colloid/gpuyukawa/colloid/omp

diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 73580ef9c0..7aa4be5208 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -729,12 +729,13 @@ potentials. Click on the style itself for a full description: "lj/cut/coul/dsf"_pair_lj.html, "lj/cut/coul/long"_pair_lj.html, "lj/cut/coul/msm"_pair_lj.html, -"lj/long/coul/long"_pair_lj_long.html, +"lj/cut/tip4p/cut"_pair_lj.html, "lj/cut/tip4p/long"_pair_lj.html, -"lj/long/tip4p/long"_pair_lj_long.html, "lj/expand"_pair_lj_expand.html, "lj/gromacs"_pair_gromacs.html, "lj/gromacs/coul/gromacs"_pair_gromacs.html, +"lj/long/coul/long"_pair_lj_long.html, +"lj/long/tip4p/long"_pair_lj_long.html, "lj/smooth"_pair_lj_smooth.html, "lj/smooth/linear"_pair_lj_smooth_linear.html, "lj96/cut"_pair_lj96.html, @@ -890,6 +891,7 @@ package"_Section_accelerate.html. "lj/cut/gpu"_pair_lj.html, "lj/cut/omp"_pair_lj.html, "lj/cut/opt"_pair_lj.html, +"lj/cut/tip4p/cut/omp"_pair_lj.html, "lj/cut/tip4p/long/omp"_pair_lj.html, "lj/cut/tip4p/long/opt"_pair_lj.html, "lj/expand/cuda"_pair_lj_expand.html, diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 9d20970018..dda14dee15 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -6398,16 +6398,16 @@ then a kspace style must also be used.
The atom style defined does not have this attribute. -
Pair style lj/cut/coul/long/tip4p requires atom IDs +
Pair style lj/cut/tip4p/long requires atom IDs
There are no atom IDs defined in the system and the TIP4P potential requires them to find O,H atoms with a water molecule. -
Pair style lj/cut/coul/long/tip4p requires atom attribute q +
Pair style lj/cut/tip4p/long requires atom attribute q
The atom style defined does not have these attributes. -
Pair style lj/cut/coul/long/tip4p requires newton pair on +
Pair style lj/cut/tip4p/long requires newton pair on
This is because the computation of constraint forces within a water molecule adds forces to atoms owned by other processors. @@ -8020,7 +8020,7 @@ variable doc page for ideas on how to make this work.
Self-explanatory. -
Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p +
Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long
This is because LAMMPS does not compute the Lennard-Jones interactions with these particles for efficiency reasons. diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt index 6e51fab09a..cd6ff024e6 100644 --- a/doc/Section_errors.txt +++ b/doc/Section_errors.txt @@ -6394,16 +6394,16 @@ The atom style defined does not have this attribute. :dd The atom style defined does not have this attribute. :dd -{Pair style lj/cut/coul/long/tip4p requires atom IDs} :dt +{Pair style lj/cut/tip4p/long requires atom IDs} :dt There are no atom IDs defined in the system and the TIP4P potential requires them to find O,H atoms with a water molecule. :dd -{Pair style lj/cut/coul/long/tip4p requires atom attribute q} :dt +{Pair style lj/cut/tip4p/long requires atom attribute q} :dt The atom style defined does not have these attributes. :dd -{Pair style lj/cut/coul/long/tip4p requires newton pair on} :dt +{Pair style lj/cut/tip4p/long requires newton pair on} :dt This is because the computation of constraint forces within a water molecule adds forces to atoms owned by other processors. :dd @@ -8016,7 +8016,7 @@ Self-explanatory. :dd Self-explanatory. :dd -{Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p} :dt +{Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long} :dt This is because LAMMPS does not compute the Lennard-Jones interactions with these particles for efficiency reasons. :dd diff --git a/doc/Section_howto.html b/doc/Section_howto.html index a02cbd977b..d09e953e9c 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -498,7 +498,7 @@ angle style of harmonic or charmm should also be used.

A TIP4P model is run with LAMMPS using two commands:

-